This looks the same as the problem I have.

I had another OS installed on the disk before I installed Ubuntu using
the 12.10 live CD.  There was a small primary partition, the rest of the
disk was an extended partition.  There were two partitions at the front
of the extended space so I installed Ubuntu at the end of the extended
space.  It seemed that everything was normal (for a few months) until I
tried to change the swap partition size.  When I started gparted it
listed all of the disk as free space.  The last time any changes were
made to the partition tables was the Ubuntu install.

As I see the problem the install changed the end of the extended
partition to an incorrect value.

During the install I used whatever partitioning program the install
uses.  The first partition defined was /home then swap then root, all at
the end of the free space.  The following is the output of fdisk.

Disk /dev/sda: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk identifier: 0xdf5ee111

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *          63       16064        8001    a  OS/2 Boot Manager
Partition 1 does not start on physical sector boundary.
/dev/sda4           16065   703309823   351646879+   5  Extended
Partition 4 does not start on physical sector boundary.
/dev/sda5           16128    10265534     5124703+   7  HPFS/NTFS/exFAT
/dev/sda6        10265598    30748409    10241406    b  W95 FAT32
Partition 6 does not start on physical sector boundary.
/dev/sda7       781461504   976771071    97654784   83  Linux
/dev/sda8       703324160   781449215    39062528   82  Linux swap / Solaris
/dev/sda9       625184768   703309823    39062528   83  Linux

The Ubuntu partitions are listed backwards.  Notice that the end of sda4
is the same as sda9, this is wrong.

Why would any program change the end of the extended partition end
unless you were purposely changing the size of the extended partition?

I changed the end of sda4 to 976773166 which I think is correct (if not
what should it be?) and now gparted can display all the partitions on
the disk and I could change the size of the swap partition.

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https://bugs.launchpad.net/bugs/812907

Title:
  Unallocated free space after creating parititons

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